Positive effects of public breeding on US rice yields under future climate scenarios.

In this study, we model and predict rice yields by integrating molecular marker variation, varietal productivity, and climate, focusing on the Southern U.S. rice-growing region.

International agreements and the plant genetics research community: A guide to practice.

Plant genetic resources (PGR), including collections held in national and international gene banks, provide access to a wide array of genetic diversity and are critical to genomics research, conservation efforts, and applied breeding. Yet, there is a general lack of awareness in the research community about the rules and treaties that govern the use of PGR, about access and benefit sharing obligations contained in international treaties and/or national laws, and about how best to comply with potentially applicable requirements. This article provides a brief history and overview of three key international agreements, namely the Convention on Biological Diversity, the Nagoya Protocol, and the International Treaty on Plant Genetic Resources for Food and Agriculture, which collectively address responsibilities and obligations related to the use of much of the world's PGR.

, an E3 ubiquitin ligase, is responsible for loss of awns during African rice domestication.

Two species of rice have been independently domesticated from different ancestral wild species in Asia and Africa. Comparison of mutations that underlie phenotypic and physiological alterations associated with domestication traits in these species gives insights into the domestication history of rice in both regions. Asian cultivated rice, and African cultivated rice, , have been modified and improved for common traits beneficial for humans, including erect plant architecture, nonshattering seeds, nonpigmented pericarp, and lack of awns.

Genome wide association analysis of root hair traits in rice reveals novel genomic regions controlling epidermal cell differentiation.

Background: Genome wide association (GWA) studies demonstrate linkages between genetic variants and traits of interest. Here, we tested associations between single nucleotide polymorphisms (SNPs) in rice (Oryza sativa) and two root hair traits, root hair length (RHL) and root hair density (RHD). Root hairs are outgrowths of single cells on the root epidermis that aid in nutrient and water acquisition and have also served as a model system to study cell differentiation and tip growth.

Identifying genes associated with abiotic stress tolerance suitable for CRISPR/Cas9 editing in upland rice cultivars adapted to acid soils.

Five genes of large phenotypic effect known to confer abiotic stress tolerance in rice were selected to characterize allelic variation in commercial Colombian upland rice cultivars adapted to drought-prone acid soil environments (cv. Llanura11 and Porvenir12). Allelic variants of the genes , , , , and were characterized by PCR and/or Sanger sequencing in the two upland cultivars and compared with the Nipponbare and other reference genomes.

Development and validation of an optimized marker set for genomic selection in southern U.S. rice breeding programs.

The potential of genomic selection (GS) to increase the efficiency of breeding programs has been clearly demonstrated; however, the implementation of GS in rice (Oryza sativa L.) breeding programs has been limited. In recent years, efforts have begun to work toward implementing GS into the Louisiana State University (LSU) Agricultural Center rice breeding program.

Can biochemical traits bridge the gap between genomics and plant performance? A study in rice under drought.

The possibility of introducing metabolic/biochemical phenotyping to complement genomics-based predictions in breeding pipelines has been considered for years. Here we examine to what extent and under what environmental conditions metabolic/biochemical traits can effectively contribute to understanding and predicting plant performance. In this study, multivariable statistical models based on flag leaf central metabolism and oxidative stress status were used to predict grain yield (GY) performance for 271 indica rice (Oryza sativa) accessions grown in the field under well-watered and reproductive stage drought conditions.

Reap the crop wild relatives for breeding future crops.

Crop wild relatives (CWRs) have provided breeders with several 'game-changing' traits or genes that have boosted crop resilience and global agricultural production. Advances in breeding and genomics have accelerated the identification of valuable CWRs for use in crop improvement. The enhanced genetic diversity of breeding pools carrying optimum combinations of favorable alleles for targeted crop-growing regions is crucial to sustain genetic gain.

Genetic architecture of root and shoot ionomes in rice (Oryza sativa L.).

Association analysis for ionomic concentrations of 20 elements identified independent genetic factors underlying the root and shoot ionomes of rice, providing a platform for selecting and dissecting causal genetic variants. Understanding the genetic basis of mineral nutrient acquisition is key to fully describing how terrestrial organisms interact with the non-living environment. Rice (Oryza sativa L.

Addressing Research Bottlenecks to Crop Productivity.

Asymmetry of investment in crop research leads to knowledge gaps and lost opportunities to accelerate genetic gain through identifying new sources and combinations of traits and alleles. On the basis of consultation with scientists from most major seed companies, we identified several research areas with three common features: (i) relatively underrepresented in the literature; (ii) high probability of boosting productivity in a wide range of crops and environments; and (iii) could be researched in 'precompetitive' space, leveraging previous knowledge, and thereby improving models that guide crop breeding and management decisions. Areas identified included research into hormones, recombination, respiration, roots, and source-sink, which, along with new opportunities in phenomics, genomics, and bioinformatics, make it more feasible to explore crop genetic resources and improve breeding strategies.

Genetic mapping identifies a rice naringenin O-glucosyltransferase that influences insect resistance.

Naringenin, the biochemical precursor for predominant flavonoids in grasses, provides protection against UV damage, pathogen infection and insect feeding. To identify previously unknown loci influencing naringenin accumulation in rice (Oryza sativa), recombinant inbred lines derived from the Nipponbare and IR64 cultivars were used to map a quantitative trait locus (QTL) for naringenin abundance to a region of 50 genes on rice chromosome 7. Examination of candidate genes in the QTL confidence interval identified four predicted uridine diphosphate-dependent glucosyltransferases (Os07g31960, Os07g32010, Os07g32020 and Os07g32060).

Corrigendum: A Coordinated Suite of Wild-Introgression Lines in and Elite Backgrounds.

[This corrects the article DOI: 10.3389/fpls.2020.

Multiple Small-Effect Alleles of Origin Enhance High Iron-Associated Stress Tolerance in Rice Under Field Conditions in West Africa.

Understanding the genetics of field-based tolerance to high iron-associated (HIA) stress in rice can accelerate the development of new varieties with enhanced yield performance in West African lowland ecosystems. To date, few field-based studies have been undertaken to rigorously evaluate rice yield performance under HIA stress conditions. In this study, two NERICA × bi-parental rice populations and one diversity panel consisting of 296 rice accessions were evaluated for grain yield and leaf bronzing symptoms over multiple years in four West African HIA stress and control sites.

A Coordinated Suite of Wild-Introgression Lines in and Elite Backgrounds.

Rice, L., is a cultivated, inbreeding species that serves as the staple food for the largest number of people on earth. It has two strongly diverged varietal groups, and , which result from a combination of natural and human selection.

Genome wide association studies for japonica rice resistance to blast in field and controlled conditions.

Background: Rice blast, caused by the fungus Pyricularia oryzae, represents the most damaging fungal disease of rice worldwide. Utilization of rice resistant cultivars represents a practical way to control the disease. Most of the rice varieties cultivated in Europe and several other temperate regions are severely depleted of blast resistance genes, making the identification of resistant sources in genetic background adapted to temperate environments a priority.

Low Additive Genetic Variation in a Trait Under Selection in Domesticated Rice.

Quantitative traits are important targets of both natural and artificial selection. The genetic architecture of these traits and its change during the adaptive process is thus of fundamental interest. The fate of the additive effects of variants underlying a trait receives particular attention because they constitute the genetic variation component that is transferred from parents to offspring and thus governs the response to selection.

An improved 7K SNP array, the C7AIR, provides a wealth of validated SNP markers for rice breeding and genetics studies.

Single nucleotide polymorphisms (SNPs) are highly abundant, amendable to high-throughput genotyping, and useful for a number of breeding and genetics applications in crops. SNP frequencies vary depending on the species and populations under study, and therefore target SNPs need to be carefully selected to be informative for each application. While multiple SNP genotyping systems are available for rice (Oryza sativa L.

Strategies for Effective Use of Genomic Information in Crop Breeding Programs Serving Africa and South Asia.

Much of the world's population growth will occur in regions where food insecurity is prevalent, with large increases in food demand projected in regions of Africa and South Asia. While improving food security in these regions will require a multi-faceted approach, improved performance of crop varieties in these regions will play a critical role. Current rates of genetic gain in breeding programs serving Africa and South Asia fall below rates achieved in other regions of the world.

Bridging old and new: diversity and evaluation of high iron-associated stress response of rice cultivated in West Africa.

Adoption of rice varieties that perform well under high iron-associated (HIA) stress environments can enhance rice production in West Africa. This study reports the genetic characterization of 323 rice accessions and breeding lines cultivated in West Africa using genotyping-by-sequencing and their phenotypic response to HIA treatments in hydroponic solution (1500 mg l-1 FeSO4·7H2O) and hot-spot fields. The germplasm consisted of four genetic subpopulations: Oryza glaberrima (14%), O.

Association mapping and genetic dissection of drought-induced canopy temperature differences in rice.

Drought-stressed plants display reduced stomatal conductance, which results in increased leaf temperature by limiting transpiration. In this study, thermal imaging was used to quantify the differences in canopy temperature under drought in a rice diversity panel consisting of 293 indica accessions. The population was grown under paddy field conditions and drought stress was imposed for 2 weeks at flowering.